I would like to be able to easily set molecules in different VMD instances
that are different sizes into different sized windows and have them all be
on the same scale. If the molecules happen to have sufficient elements in
common, I can use the method below (based on a much appreciated suggestion
by Jodi). But it would be nicer to have another way. Is it possible to
set a scale such as "1 angstrom = 20 px"?

Here's my slight variant of J's suggestion:

1. Enable a view of some subset of common parts of the final molecular
views of all molecules

2. Open the TkConsole in each VMD instance

3. Determine reasonable relative window sizes and scalings so that
everything you finally want to see fits. Here, let's say that molecule 1
(M1) needs about twice the height of molecule 2 (M2) and that you want the
width the same. Let's say that when the whole scene is rendered, M1 needs
to be scaled down to a quarter (0.25).